Package: ECOTOXr 1.1.1.0013

ECOTOXr: Download and Extract Data from US EPA's ECOTOX Database

The US EPA ECOTOX database is a freely available database with a treasure of aquatic and terrestrial ecotoxicological data. As the online search interface doesn't come with an API, this package provides the means to easily access and search the database in R. To this end, all raw tables are downloaded from the EPA website and stored in a local SQLite database <doi:10.1016/j.chemosphere.2024.143078>.

Authors:Pepijn de Vries [aut, cre, dtc]

ECOTOXr_1.1.1.0013.tar.gz
ECOTOXr_1.1.1.0013.zip(r-4.5)ECOTOXr_1.1.1.0013.zip(r-4.4)ECOTOXr_1.1.1.0013.zip(r-4.3)
ECOTOXr_1.1.1.0013.tgz(r-4.5-any)ECOTOXr_1.1.1.0013.tgz(r-4.4-any)ECOTOXr_1.1.1.0013.tgz(r-4.3-any)
ECOTOXr_1.1.1.0013.tar.gz(r-4.5-noble)ECOTOXr_1.1.1.0013.tar.gz(r-4.4-noble)
ECOTOXr_1.1.1.0013.tgz(r-4.4-emscripten)ECOTOXr_1.1.1.0013.tgz(r-4.3-emscripten)
ECOTOXr.pdf |ECOTOXr.html✨
ECOTOXr/json (API)
NEWS

# Install 'ECOTOXr' in R:
install.packages('ECOTOXr', repos = c('https://pepijn-devries.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/pepijn-devries/ecotoxr/issues

Pkgdown site:https://pepijn-devries.github.io

On CRAN:

Conda:

6.20 score 10 stars 6 scripts 419 downloads 29 exports 56 dependencies

Last updated 1 hours agofrom:99fffc2705 (on main). Checks:9 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 11 2025
R-4.5-winOKMar 11 2025
R-4.5-macOKMar 11 2025
R-4.5-linuxOKMar 11 2025
R-4.4-winOKMar 11 2025
R-4.4-macOKMar 11 2025
R-4.4-linuxOKMar 11 2025
R-4.3-winOKMar 11 2025
R-4.3-macOKMar 11 2025

Exports:as_date_ecotoxas_numeric_ecotoxas_unit_ecotoxas.casbuild_ecotox_sqlitecascheck_ecotox_availabilitycheck_ecotox_buildcheck_ecotox_versioncite_ecotoxdbConnectEcotoxdbDisconnectEcotoxdownload_ecotox_dataget_ecotox_infoget_ecotox_pathget_ecotox_sqlite_fileget_ecotox_urlis.caslist_ecotox_fieldslist_ecotox_web_fieldsprocess_ecotox_datesprocess_ecotox_numericsprocess_ecotox_unitssearch_ecotoxsearch_ecotox_lazysearch_query_ecotoxshow.caswebsearch_comptoxwebsearch_ecotox

Dependencies:askpassbitbit64blobcachemcellrangerclicliprcpp11crayoncurlDBIdbplyrdplyrfansifastmapgenericsgluehmshttrhttr2jsonlitelifecyclemagrittrmemoisemimeopensslpillarpkgconfigplogrprettyunitsprogresspurrrR6rappdirsRcppreadrreadxlrematchrlangRSQLitervestselectrstringistringrsystibbletidyrtidyselecttzdbunitsutf8vctrsvroomwithrxml2

ECOTOX database schema

Rendered fromecotox-schema.Rmdusingknitr::rmarkdownon Mar 11 2025.

Last update: 2025-02-19
Started: 2025-02-16

Reproducibility

Rendered fromreproducibility.Rmdusingknitr::rmarkdownon Mar 11 2025.

Last update: 2025-02-19
Started: 2025-02-19

Sanitising ECOTOX

Rendered fromsanitising-ecotox.Rmdusingknitr::rmarkdownon Mar 11 2025.

Last update: 2025-03-11
Started: 2025-03-11

Searching ECOTOX

Rendered fromsearching-ecotox.Rmdusingknitr::rmarkdownon Mar 11 2025.

Last update: 2025-02-19
Started: 2025-02-12

Readme and manuals

Help Manual

Help pageTopics
Values represented by ECOTOX 'character' to datesas_date_ecotox
Values represented by ECOTOX 'character' to 'numeric'as_numeric_ecotox
Text from the ECOTOX database to 'mixed_units'as_unit_ecotox
Build an SQLite database from zip archived tables downloaded from EPA websitebuild_ecotox_sqlite
Functions for handling chemical abstract service (CAS) registry numbersas.cas as.character.cas as.data.frame.cas as.double.cas as.integer.cas as.list.cas c.cas cas format.cas is.cas print.cas show.cas [.cas [<-.cas [[.cas [[<-.cas
Check whether a ECOTOX database exists locallycheck_ecotox_availability
Check the locally build database for validitycheck_ecotox_build
Check if the locally build database is up to datecheck_ecotox_version
Cite the downloaded copy of the ECOTOX databasecite_ecotox
Open or close a connection to the local ECOTOX databasedbConnectEcotox dbDisconnectEcotox
Download and extract ECOTOX database files and compose databasedownload_ecotox_data
Get information on the local ECOTOX database when availableget_ecotox_info
The local path to the ECOTOX database (directory or sqlite file)get_ecotox_path get_ecotox_sqlite_file
Get ECOTOX download URL from EPA websiteget_ecotox_url
List the field names that are available from the ECOTOX databaselist_ecotox_fields
Process ECOTOX search results by converting 'character' to dates where relevantprocess_ecotox_dates
Process ECOTOX search results by converting 'character' to 'numeric' where relevantprocess_ecotox_numerics
Process ECOTOX search results by converting 'character' to units where relevantprocess_ecotox_units
Search and retrieve toxicity records from the databasesearch_ecotox search_ecotox_lazy search_query_ecotox
Search and retrieve substance information from <https://comptox.epa.gov/dashboard>websearch_comptox
Search and retrieve toxicity records from the online databaselist_ecotox_web_fields websearch_ecotox